Coral Holobiont Physiology under OA/OW
Model selection for physiology
Physiological response parameters were assessed using mixed-effects linear models across species and treatments. Model selection was carried out using backward elimination of random-effects followed by fixed-effects using the package lmerTest (version 3.1.3)
Protein
While value ~ species + fpco2 + ftemp + (1 | colony) + species:ftemp was the best-fit model structure identified, we wanted to model both pCO2 and temperature responses by species so moving forward we are using the following model structure:
value ~ species * (fpco2 + ftemp) + (1 | colony)
Figure:
Carbohydrate
While value ~ species + ftemp was the best-fit model structure identified, we wanted to model responses with a random effect of colony so moving forward we are using the following model structure:
value ~ species * (fpco2 + ftemp) + (1 | colony)
Figure:
Lipid
While value ~ species + ftemp + reef + species:ftemp + species:reef was the best-fit model structure identified, we wanted to model both pCO2 and temperature responses by species and with random effect of colony so moving forward we are using the following model structure:
value ~ species * (fpco2 + ftemp) + reef + species:reef + (1 | colony)
Figure:
Density
While value ~ species + fpco2 + ftemp + reef + (1 | colony) + species:fpco2 + species:ftemp + fpco2:ftemp + species:reef + fpco2:reef + ftemp:reef + species:fpco2:ftemp + species:fpco2:reef + species:ftemp:reef + fpco2:ftemp:reef + species:fpco2:ftemp:reef was the best-fit model structure identified, we wanted to model both pCO2 and temperature responses by species and with random effect of colony so moving forward we are using the following model structure:
value ~ species * (fpco2 + ftemp) + reef + species:reef + (1 | colony)
Figure:
Chlorophyll
Since the best-fit model fits our design, we will proceed with the following model structure:
value ~ species + fpco2 + ftemp + reef + (1 | colony) + species:fpco2 + species:ftemp + fpco2:ftemp + species:reef
Figure:
Total Host
Since the best-fit model fits our design, we will proceed with the following model structure:
value ~ species + fpco2 + ftemp + reef + (1 | colony) + species:fpco2 + species:ftemp + species:reef + fpco2:reef + species:fpco2:reef
Figure:
Calcification
This is the same model from Bove et al 2019, just matching aesthetics for this manuscript.
Figure 1
Figure 1. Modeled 95% confidence interval of (A) total host energy reserves (mg cm-2), (B) cell density (106 cells cm-2), and (C) Chlorophyll a (ug cm-2) for S. siderea, P. strigosa, and P. astreoides at T0 (green) or T90 (red/blue), with individual coral fragment physiology denoted by points. Blue denotes 28°C and red denotes 31°C, with pCO2 treatment along the x axis.
Correlation assessments
Here, I am exploring the relationships between each physiology parameter measured above.
Figure 2. Correlation matrix for S. siderea, P. strigosa, and P. astreoides depicting pair-wise comparisons of physiological parameters within each species. Colour and ellipse width denote R2 of each significant comparison, and blank grids represent non-significant pair-wise comparisons (P > 0.05).Each parameter is denoted in blue text along the diagonal of each plot. Correlations with R2 above 0.5 (shown in orange and red in matrix plot) are explored further below.
Siderastrea siderea
Pseudodiploria strigosa
Porites astreoides
Holobiont PCAs
Siderastrea siderea
##
## Call:
## adonis(formula = value ~ reef + ftemp + fpco2, data = s_df_l, method = "eu")
##
## Permutation: free
## Number of permutations: 999
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## reef 1 677 677.1 0.4564 0.00082 0.486
## ftemp 1 2939 2939.3 1.9810 0.00355 0.151
## fpco2 3 14491 4830.3 3.2556 0.01750 0.024 *
## Residuals 546 810104 1483.7 0.97814
## Total 551 828211 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Pseudodiploria strigosa
##
## Call:
## adonis(formula = value ~ reef + ftemp + fpco2, data = p_df_l, method = "eu")
##
## Permutation: free
## Number of permutations: 999
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## reef 1 10809 10809.2 3.4558 0.00709 0.065 .
## ftemp 1 18776 18775.5 6.0027 0.01231 0.012 *
## fpco2 3 31998 10666.2 3.4100 0.02098 0.015 *
## Residuals 468 1463839 3127.9 0.95963
## Total 473 1525422 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Porites astreoides
##
## Call:
## adonis(formula = value ~ reef + ftemp + fpco2, data = a_df_l, method = "eu")
##
## Permutation: free
## Number of permutations: 999
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## reef 1 137 136.6 0.1277 0.00030 0.714
## ftemp 1 4808 4808.4 4.4961 0.01062 0.036 *
## fpco2 3 11590 3863.2 3.6123 0.02559 0.013 *
## Residuals 408 436336 1069.5 0.96349
## Total 413 452871 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Figure 2
Plasticity analyses
This is still being updated at the moment
## R version 3.5.1 (2018-07-02)
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## Running under: macOS High Sierra 10.13.6
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